Hi John, mri_segstats is the right thing to do. It doesn't rerun the segmentation, but if you rerun the command you find can in the scripts/recon-all.log file it will do things like correct for partial volume effects, which is a big deal in the hippocampus.
cheers Bruce On Thu, 23 Dec 2010, McLean John (NHS Greater Glasgow & Clyde) wrote: > Hi, > > I have ran recon-all and got the Hippocampal volumes I desire from the > aseg.stats file. However, I have manually refined some of the volumes using > the tkmedit segmentation tool brushes and I now need to extract the revised > volume estimates. > > I believe I can run 'mri_segstats' to obtain the revised volume, this seems > to run the full segmentation process again, would this be the recommended way > of obtaining the revised volumes or if I'm only interested in the Hippocampal > volume is there a more precise command I could run to extract only this from > my revised aseg.mgz segmentation file? > > Many Thanks > John McLean > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take > any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff > in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > For more information and to find out how you can switch, visit > www.connectingforhealth.nhs.uk/nhsmail > > ******************************************************************************************************************** > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
